From my understanding, the rumored father and son game from Kojima was just the result of a misunderstanding. In an interview he said he was thinking of making a Gamecube title and that his next project would have something to do with father and son.
Basically, they were two seperate thoughts and, with the latter, he just met he was going to take some time off to spend with his family. It was just a figure of speech that some people didn't take figuratively.